I've made some progress in getting the vertical windows, through commenting out lines 937 though 1008, and from changing 1123 & 1124 to:
JavaScript:
Window_CTB.prototype.initialize = function(y, opacity) {
Window_Base.prototype.initialize.call(this, 1020, y - 3, ctb_window_width, ctb_window_height);
However, only the windows at the bottom appear. I've moved the whole array of windows around, but only the two near the status window will appear.
EDIT: Okay, I ended up undoing the line 937-1008 commenting out, but resizing the log and help windows allow the CBT windows to display properly. Only issue is figuring out the spacing.
EDIT II: Aaand I fixed the spacing by changing line 1107 to:
JavaScript:
this._turnOrderWindows.push(new Window_CTB(ctb_window_x_offset + index * (ctb_window_width * 2/3), opacity));